During summer thermal stratification, a broad transition zone with hypoxic conditions is formed in meromictic ferruginous Lake Kuznechikha between the thermocline and the main gradient of water mineralization. In this zone, the chemical composition of water undergoes an ecologically significant transformation due to overlapping gradients of nutrient concentrations and redox conditions. We present an analysis of a strongly vertically structured community of prokaryotic and eukaryotic phototrophs developing in the lake as a whole and especially in the transition zone. In early summer 2009, a sequence of phototrophic organisms with depth in order Chlorophyceae → Chromatiales → Chloroflexales → Euglenales → Chlorobiales was observed in the transition zone, while cyanobacteria were almost completely absent. Biomass maximum of anoxygenic phototrophic bacteria was located between the peaks of phototrophic picoplankton and euglenoids. Such a coexistence of oxygenic and anoxygenic phototrophs in a wide range of depths is highly unusual and sharply distinguishes Lake Kuznechikha from waterbodies with sulphide-containing monimolimnion.

The characteristics of micro-scale vertical heterogeneity of physicochemical parameters, photosynthetic pigments’ content and populations of phototrophic microbial plankton in four karst lakes of the Mari-Chodra NP (rep. Mari El), the Bolshoy Kichier, Cherny Kichier, Shungaldan and the Blue Oxbow, are presented on the basis of summer surveys of 2006, 2007 and 2009. According to our data, two lakes, Shungaldan and Cherny Kichier are, meromictic waterbodies of crenogenic type; the Lake Bolshoy Kichier is holomictic with stable summer stratification and anoxic hypolimnion. The Lake Blue Oxbow occupies an intermediate position, and, apparently, is irregularly mixing. The physicochemical conditions and composition of the phototrophic plankton communities of the chemocline zone of the two previously studied lakes, Bolshoy and Cherny Kichier, have remained stable over the past 20-35 years. Significant development of anoxygenic phototrophic bacteria was found in two lakes in which data on their development were previously absent. In the bacterial plates of meromictic lakes, the concentration of bacteriochlorophyll d, the pigment of green phototrophic bacteria, reaches some mg per liter.

Bacterial diversity in attached communities of the anoxic part of the Solodovka wetland (Samara region, Russia), which feeds on cold karst springs with a high (>3 mM) sulfide content was studied using high-throughput sequencing of the variable regions V3−V4 of 16S rRNA gene. The sequences were grouped into 370 operational taxonomic units (OTUs); the OTU number per sample varied within a broad range, from 52 to 277. Taxonomic diversity in the samples depended on mat type, temperature, and sulfide concentration. The highest diversity was found in typical soft cyanobacterial mats; bacterial diversity in hard microbialites was much lower. Phototrophic bacteria formed the basis of all studied communities. In the typical mats, cyanobacteria prevailed, accompanied by phototrophic Chloroflexales, the latter being responsible for 7−13% of the total number of sequences. Hard microbialites and the mat developing at the highest sulfide concentration were characterized by low representation of these taxa and a high proportion of phototrophic Proteobacteria and Chlorobiaceae. Organisms of the sulfur cycle, Desulfobacterota and Campylobacterota, predominated in the chemotrophic part of the communities. While the organisms with fermentative metabolism and facultative chemolithotrophs were represented by a large number of OTUs, they were minor in abundance, and the sequences of the phyla Actinobacteria and Acidobacteria, which are usually widespread in oxic aquatic ecosystems have not been found. In general, the chemotrophic part of the studied communities strongly resembled the attached communities from cave streams and communities of various underground aquifers. Their phototrophic component was formed relatively independently of the chemotrophic one with the participation of the surrounding surface microbiota. The sequences most similar to some of the most abundant OTUs in the Solodovka wetland originated from the chemocline of stratified lakes, including meromictic ones.

Kuibyshev Reservoir, the largest in the Volga basin, is poorly covered by modern molecular studies. The results of a metabarcoding study of pro- and eukaryotic microbial plankton in its lower section during the summer period are presented. Bacterioplankton composition was typical for most temperate freshwater bodies and characterized by the dominance of cyanobacteria, Pseudomonadota, Bacteroidota, Actinomycetota, and PVC superphylum (Verrucomicrobiota and Planctomycetota), with a somewhat increased proportion of the latter. The protist community was dominated by Cryptista, principally phototrophic, and various ciliates. Several picoeukaryotic groups were newly detected in the reservoir. A relationship between the composition of both bacterioplankton and protist communities and the stage of phytoplankton succession, including the cyanobacterial bloom, was observed. Some inconsistency between the cyanobacterial bloom phase and the structure of other parts of the microbial plankton is obviously due to some temporal delay, spatial station position, and inflow from tributaries. Heterotrophic bacterioplankton indicator species of the main bloom stage include OTUs representing both the phycosphere of colonial cyanobacteria and free-living species. Among the protists, sessile ciliates benefit most from plenty of substrates for colonization, while cyanobacterial grazers and parasites were minor. Overall, the cyanobacterial bloom creates new niches for the plankton community and significantly modifies its structure.

Persistent lake stratification is often accompanied by anoxia in the bottom layer, leading to pronounced vertical heterogeneity of microbial communities and their functional potential. We investigated the vertical distribution of bacterioplankton in two clear-water stratified lakes: Lake Palenoe (Southern boundary of the forest zone, 27 ha, 8 m deep) and Lake Prudovikov (forest-steppe zone, 6.5 ha, 5.5 m deep). Among the heterotrophic bacterioplankton, Planctomycetota and Verrucomicrobiota dominated in both lakes by relative read abundance, with Proteobacteria and Bacteroidota occupying the third and fourth positions. Common freshwater Actinomycetota and Pseudomonadota, e.g., Nanopelagicus and Planktophila (Nanopelagicales), Fonsibacter (Alphaproteobacteria), and Comamonadaceae (Betaproteobacteria), were present in both lakes at similar but low abundances. At lower taxonomic levels, the bacterioplankton of the two lakes differed substantially. Furthermore, while in the epilimnion the amplicon sequence variants (ASVs) present in one lake were substituted by different, but closely related sequences in the other, the differences between the samples from the anaerobic layers were more pronounced due to a more phylogenetically contrasting ASV structure. In general, the vertical structure of bacterioplankton in Lake Prudovikov was notably less diverse than that in Lake Palenoe. Cyanobacteria was the dominant phylum in the epilimnion of Lake Prudovikov but ranked fourth in the less productive Lake Palenoe. In both lakes, representatives of Cyanobiaceae were among the dominants. Besides, the cyanobacteria Dolichospermum spp. and Planktothrix isothrix were dominant in Lake Palenoe, while Pseudanabaena, Raphidiopsis, and Planktothrix agardhii prevailed in Lake Prudovikov. Different taxa of Cyanobacteria and Chlorobiota dominated among phototrophic bacteria in the chemocline of both lakes and the hypolimnion of Lake Palenoe; other groups were minor. Within Chromatiaceae, Thiodictyon syntrophicum was found in Lake Palenoe, whereas three ASVs belonging to Chromatium okenii (previously not recorded in this lake) and an undetermined ASV distantly related to both Thiodictyon and Lamprocystis were present in Lake Prudovikov. Despite clear differences in phylogenetic structure, analysis of PICRUSt2-predicted metabolic pathway abundances revealed functional similarities between the epilimnetic bacterial communities of both lakes. However, samples from the chemocline zone (3.5–4.0 m) and the lowest studied horizon of Lake Palenoe (6 m) differed most markedly from other samples and from each other. Our data demonstrate that functional structure remains considerably stable at high steps of the pathway hierarchy and rather contrasting at the level of predicted gene orthology structure.